Sorry for any confusion.

The problem isn't being caused by JoomSEF - it existed before JoomSEF and was hoping JoomSEF could remedy issue.Let me try again.

I have a website that I want certain components (i.e. PhocaDownload) to use a different template than the site's default template.
If I do not use Joomla's SEF (shut off the 2 settings), the new template shows fine on my PhocaDownload, however it gives the long URL with ID #'s (not something I care for).
If I turn on Joomla's 2 SEF settings, the PhocaDownload component works, but with the default template (even though I have not changed the component to use it).

My understanding was that there was an issue with Joomla's default SEF settings making it difficult to use the templates in the way I desire. I was led to believe that JoomSEF was a solution to allow the templates to show correctly by somehow fixing the SEF issue. In my flawed logic I could see shutting off Joomla's SEF and using JoomSEF to bypass it (like JoomSEF was supplementing the code) but I read that both Jooomla's and JoomSEF should be on. What settings they should be and how they relate to adding/removing ItemID's.... uhhh.... yeah. sure. not a clue :)

I honestly have a basic understanding of how the SEF stuff works, and an even smaller understanding of PHP.
If need be I'm more than happy to give you access dajo to check out how much I might have screwed stuff up. hehehhe
I'm just trying to get my wife's website running so she can sell her artwork.
Thanks again for your support. Sorry it's taking so long..... time differences suck for tech support. :)

Since the problem is not caused by JoomSEF, I can only offer you our paid support services to check your website's configuration and try to find what's causing the problem.
If you're interested, please purchase 1 hour of our support time at www.artio.net/e-shop/support-services/joomla-related-support-1h and contact me at Diese E-Mail-Adresse ist gegen Spambots geschützt! Du musst JavaScript aktivieren, damit Du sie sehen kannst. with your order number and access credentials to your website's administration area and FTP and we'll check what's causing the template problems. However since I don't know yet what's the cause, I can't promise we'll be able to fix it in the one hour time and depending on the cause there may be more time required to fix it.